Impact of Cytosine Methylation on DNA-Free-Samples for Students

Question: Discuss about the Impact of Cytosine Methylation on DNA. Answer: Translating a sentence In the sentence In addition, mCpG dinucleotides can be recognized by a specific class of proteins, the methyl-CpG domainbinding proteins, some of which can recruit histone deacetylases and are thought to promote local chromatin condensation (Yin et al. 2017), the authors is explaining the indirect effects of DNA methylation on transcription. Certain proteins such as methyl-CpG domainbinding proteins behave as structural protein and recognize and bind to mCpG dinucleotides, which in turn recruit different histone deacetylases and cause chromatin condensation and finally suppressing gene transcription. Aim of the paper The aim of the paper Impact of cytosine methylation on DNA binding specificities of human transcription factors (Yin et al. 2017) is to examine the mechanism by which methylation of the cytosine affect the binding of transcription factors to the DNA. CpG methylation has both direct and indirect effects on the transcription. The methylation of cytosine causes change in the structure of the DNA, which in turn can prevent the binding of many transcriptional factors to their recognition motifs (Schbeler 2015). This paper analyses the binding of different transcription factors to their DNA sequences. It is a systematic analysis of all the different possible DNA sequences where the transcription factors can bind and hence determining its effect on gene expression. Annotating a figure Source: Yin et al. (2017) In the left panel of the above figure, the author is systematically analysing the affinity of different fragment of transcription factors towards CpG methylation with the help of SELEX technique sensitive to methylation. Different colours are used to indicate different fractions. The mechanism is explained with the help of HOXB13gene as shown in the right panel. It explains the structure of the HOXB13gene and its affinity towards CpG methylation. Predicting conclusion From the introduction of the paper, it is possible to deduce what the author is trying to conclude. This provides a clear idea to the reader of the work of the author. As given in the introduction, one can understand that the author is analysing the effect of the methylation of cytosine on the binding of transcription factors to DNA. However, it is not possible to deduce whether such methylation process has positive or negative effects on the DNA. Hence, it helps to capture the interest of the reader till the last page of the article (Cremers and Mauw 2012). Designing an experiment In the present paper, the author has explained the effect of cytosine methylation on the binding of transcription factors. CpG methylation is widely observed in prokaryotes and eukaryotes (Capuano et al. 2014). However, the effect of methylation on other nucleotide bases is still unknown. I will employ the same methods such as bisulphite sequencing and SELEX method as used by the author to determine the methylation status on other nucleotides and its effects. The comparison of the result obtained by the author with the result of my experiment will help to understand the reason behind the affinity of methylation towards 5' position of cytosine. References Capuano, F., Mu?lleder, M., Kok, R., Blom, H.J. and Ralser, M., 2014. Cytosine DNA methylation is found in Drosophila melanogaster but absent in Saccharomyces cerevisiae, Schizosaccharomyces pombe, and other yeast species.Analytical chemistry,86(8), pp.3697-3702. Cremers, C. and Mauw, S., (2012). Introduction, inOperational Semantics and Verification of Security Protocols, Springer, Berlin Heidelberg, 1-7. Schbeler, D., 2015. Function and information content of DNA methylation.Nature,517(7534), p.321. Yin, Y., Morgunova, E., Jolma, A., Kaasinen, E., Sahu, B., Khund-Sayeed, S., Das, P.K., Kivioja, T., Dave, K., Zhong, F. and Nitta, K.R., (2017). Impact of cytosine methylation on DNA binding specificities of human transcription factors.Science,356(6337): p.eaaj2239.